Just a quick update.
It seems that my system is automatically turning off the power to a USB Root Hub (I'm hearing the Windows USB plug-in sound). What I've done is I uninstalled the HID compliant mouse on the Device Manager then made a restart. Then from the Universal Serial Bus controllers on Device Manager, I turned off the "Allow the computer to turn off this device to save power" on USB Root Hub's properties. I only turned off the first one on the list. I have seven hubs.
Right now the issue seems to be gone.
Only the scroll-wheel issue is left now. Any help will be greatly appreciated, thanks.
Update 2:
I think I found out why the USB hubs are messing around (at least in my case). I have a USB gaming headset and after plugging in a different headphone which uses a headphone jack the problem reoccur. I've disconnected the jack the the issue is gone.
Update 3:
The issue is back again. This is really frustrating.